Align Citrate:H+ symporter (characterized)
to candidate H281DRAFT_03338 H281DRAFT_03338 MFS transporter, MHS family, citrate/tricarballylate:H+ symporter
Query= TCDB::P16482 (444 letters) >FitnessBrowser__Burk376:H281DRAFT_03338 Length = 432 Score = 642 bits (1655), Expect = 0.0 Identities = 318/423 (75%), Positives = 366/423 (86%) Query: 21 TAGGARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFASLMMTFAVFGAGFL 80 ++G ++ A+ RVT+GNFLEQFDFFLFGFYAT IA FFPA SEFASLMMTFAVFGAGFL Sbjct: 9 SSGRSKAAAVFRVTAGNFLEQFDFFLFGFYATQIAKVFFPADSEFASLMMTFAVFGAGFL 68 Query: 81 MRPIGAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGLWAPLLVLIGRLLQ 140 MRP+GAIVLGAYID VGRRKGLIVTLSIMA+GT LI +P Y T+GL AP LVLIGRLLQ Sbjct: 69 MRPLGAIVLGAYIDDVGRRKGLIVTLSIMASGTILIAFVPGYATLGLLAPALVLIGRLLQ 128 Query: 141 GFSAGAELGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGFALNAVLEPSAISD 200 GFSAGAELGGVSVYLAE+ATPGRKGF+TSWQS SQQVAI+VAAA+GFALN + + I+ Sbjct: 129 GFSAGAELGGVSVYLAEMATPGRKGFFTSWQSASQQVAIVVAAALGFALNQSMSAATIAS 188 Query: 201 WGWRIPFLFGVLIVPFIFILRRKLEETQEFTARRHHLAMRQVFATLLANWQVVIAGMMMV 260 WGWR+PF G +IVPFIF+LRR L+ET+EF AR+H +M++VF TL+ NW VVIAGMM+V Sbjct: 189 WGWRVPFFVGCMIVPFIFMLRRNLQETEEFKARQHRPSMKEVFRTLVQNWTVVIAGMMLV 248 Query: 261 AMTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVGGALSDRFGRRSVL 320 AMTT +FYLITVYAPTFGK VL LS +DSLLVTL VA+SNF WLP+GGALSD+ GRR +L Sbjct: 249 AMTTASFYLITVYAPTFGKTVLHLSTADSLLVTLCVAVSNFVWLPIGGALSDKLGRRPLL 308 Query: 321 IAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIPALTEIMPAEVRVA 380 +AMT+LA+ATA+PAL++LA+APSFL ML LLWLSF+YG+YNGAM+ ALTE+MPA+VRVA Sbjct: 309 VAMTVLAIATAYPALSLLAHAPSFLNMLLALLWLSFMYGIYNGAMVVALTEVMPAQVRVA 368 Query: 381 GFSLAYSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFAAICGLLATCYLYRRSAVAL 440 GFSLAYSLATAVFGGFTP ISTALI TGDKA+PGYWMSFAA C L+AT LYRR A L Sbjct: 369 GFSLAYSLATAVFGGFTPAISTALIHMTGDKAAPGYWMSFAAACALMATFALYRRRATTL 428 Query: 441 QTA 443 A Sbjct: 429 TPA 431 Lambda K H 0.329 0.139 0.421 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 679 Number of extensions: 25 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 444 Length of database: 432 Length adjustment: 32 Effective length of query: 412 Effective length of database: 400 Effective search space: 164800 Effective search space used: 164800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory